In vitro selection of DNA-based aptamers that exhibit RNA-like conformations using a chimeric oligonucleotide library that contains two different xeno-nucleic acids

Abstract

We successfully generated chimeric DNA aptamers that contained six nucleoside analogs of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) in the primer region and multiple guanosine analogs of 2'-deoxy-2'-fluoro-ribonucleic acid (FNA) in the non-primer region using capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX). Active species enrichment became saturated only after five selection rounds, and we obtained DNA-based xeno-nucleic acid (XNA) aptamers that had high binding affinities for the target human thrombin, with dissociation constant (Kd) values of ≥10 nanomolar. Based on sequence and circular dichroism (CD) analyses, these XNA aptamers exhibited RNA-like conformations, which could cause DNA-based strands to adopt structurally diverse conformations.

Specific Light-Up System for Protein and Metabolite Targets Triggered by Initiation Complex Formation

“…P 1 -thr-PS remained substantially intact in 10% v/v human serum for 2 h at 37 °C while P 1 -thr was almost entirely digested (Figure S8 ). These results indicate that further chemical modifications of the nucleotide components used for SATIC will yield better detection systems 29 , 33 – 36 .…”

Selection, Characterization and Application of Artificial DNA Aptamer Containing Appended Bases with Sub-nanomolar Affinity for a Salivary Biomarker

“…In particular, when modified DNA/RNA is used as a library181920212223242526272837383940, the success or failure of the selection can greatly depend on the polymerase used, which affects the accuracy of modified nucleotide incorporation and the efficiency of modified oligonucleotides production4142434445. In 2001, Sawai et al .…”

Pseudo aptamer expands aptamer’s applications

“…The incorporation of BNAs into oligonucleotides allows the production of modified synthetic oligonucleotides with higher binding affinity against DNA or RNA, better selectivity, stronger and more sequence selective triplex-forming characters, pronounced hi- gher nuclease resistance than Sp-phosphorothioate analogues, as well as better water solubility. [106][107][108] A new type of BNA analogs were designed by taking the length of the bridged bonds into account. A six-membered bridged structure with a unique structural feature (N-O bond) in the sugar moiety was designed to insert a nitrogen atom.…”